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2023
The evolutionary mechanism of non-carbapenemase carbapenem-resistant phenotypes in Klebsiella spp
Rosas, N. C., Wilksch, J., Barber, J., Li, J., Wang, Y., Sun, Z., Rocker, A., Webb, C. T., Perlaza-Jiménez, L., Stubenrauch, C. J., Dhanasekaran, V., Song, J., Taiaroa, G., Davies, M., Strugnell, R. A., Bao, Q., Zhou, T., McDonald, M. J. & Lithgow, T., 6 Jul 2023, In: eLife. 12, 27 p., e83107.Research output: Contribution to journal › Article › Research › peer-review
Open Access11 Link opens in a new tab Citations (Scopus) -
2022
A Structurally Characterized Staphylococcus aureus Evolutionary Escape Route from Treatment with the Antibiotic Linezolid
Perlaza-Jiménez, L., Tan, K. S., Piper, S. J., Johnson, R. M., Bamert, R. S., Stubenrauch, C. J., Wright, A., Lupton, D., Lithgow, T. & Belousoff, M. J., Jul 2022, In: Microbiology Spectrum. 10, 4, 11 p., e0058322.Research output: Contribution to journal › Article › Research › peer-review
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PreAcrs: a machine learning framework for identifying anti-CRISPR proteins
Zhu, L., Wang, X., Li, F. & Song, J., Dec 2022, In: BMC Bioinformatics. 23, 1, 21 p., 444.Research output: Contribution to journal › Article › Research › peer-review
Open Access15 Link opens in a new tab Citations (Scopus) -
Tall tails: Cryo-electron microscopy of phage tail DNA ejection conduits
Hardy, J. M., Dunstan, R. A., Lithgow, T. & Coulibaly, F., Feb 2022, In: Biochemical Society Transactions. 50, 1, p. 459-471 13 p.Research output: Contribution to journal › Review Article › Research › peer-review
Open Access31 Link opens in a new tab Citations (Scopus) -
2021
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features
Zhu, Y.-H., Hu, J., Ge, F., Li, F., Song, J., Zhang, Y. & Yu, D.-J., 20 May 2021, In: Briefings in Bioinformatics. 22, 3, 14 p., bbaa076.Research output: Contribution to journal › Article › Research › peer-review
20 Link opens in a new tab Citations (Scopus) -
AcrHub: an integrative hub for investigating, predicting and mapping anti-CRISPR proteins
Wang, J., Dai, W., Li, J., Li, Q., Xie, R., Zhang, Y., Stubenrauch, C. & Lithgow, T., 8 Jan 2021, In: Nucleic Acids Research. 49, D1, p. D630-D638 9 p.Research output: Contribution to journal › Article › Research › peer-review
Open Access37 Link opens in a new tab Citations (Scopus) -
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria
Wang, J., Li, J., Hou, Y., Dai, W., Xie, R., Marquez-Lago, T. T., Leier, A., Zhou, T., Torres, V., Hay, I., Stubenrauch, C., Zhang, Y., Song, J. & Lithgow, T., 8 Jan 2021, In: Nucleic Acids Research. 49, D1, p. D651-D659 9 p.Research output: Contribution to journal › Article › Research › peer-review
Open Access42 Link opens in a new tab Citations (Scopus) -
Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework
Li, F., Chen, J., Ge, Z., Wen, Y., Yue, Y., Hayashida, M., Baggag, A., Bensmail, H. & Song, J., 1 Mar 2021, In: Briefings in Bioinformatics. 22, 2, p. 2126-2140 15 p.Research output: Contribution to journal › Article › Research › peer-review
66 Link opens in a new tab Citations (Scopus) -
DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites
Liu, Q., Chen, J., Wang, Y., Li, S., Jia, C., Song, J. & Li, F., 1 Jul 2021, In: Briefings in Bioinformatics. 22, 3, 14 p., bbaa124.Research output: Contribution to journal › Article › Research › peer-review
110 Link opens in a new tab Citations (Scopus) -
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy
Xie, R., Li, J., Wang, J., Dai, W., Leier, A., Marquez-Lago, T. T., Akutsu, T., Lithgow, T., Song, J. & Zhang, Y., 20 May 2021, In: Briefings in Bioinformatics. 22, 3, 15 p., bbaa125.Research output: Contribution to journal › Article › Research › peer-review
76 Link opens in a new tab Citations (Scopus) -
Mechanistic Insights into the Capsule-Targeting Depolymerase from a Klebsiella pneumoniae Bacteriophage
Dunstan, R. A., Bamert, R. S., Belousoff, M. J., Short, F. L., Barlow, C. K., Pickard, D. J., Wilksch, J. J., Schittenhelm, R. B., Strugnell, R. A., Dougan, G. & Lithgow, T., 3 Sept 2021, In: Microbiology Spectrum. 9, 1, 15 p., e01023-21.Research output: Contribution to journal › Article › Research › peer-review
Open Access67 Link opens in a new tab Citations (Scopus) -
Stepwise evolution of carbapenem-resistance, captured in patient samples and evident in global genomics of Klebsiella pneumoniae
Perlaza-Jimenez, L., Wilksch, J. J., Stubenrauch, C. J., Chen, T., Zhao, Y., Zhou, T., Lithgow, T. & Dhanasekaran, V., 25 Jun 2021, medRxiv preprints, 2021 28 p.Research output: Contribution to specialist publication › Article › Research
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The Carbapenemase BKC-1 from Klebsiella pneumoniae Is Adapted for Translocation by Both the Tat and Sec Translocons
Bharathwaj, M., Webb, C. T., Vadlamani, G., Stubenrauch, C. J., Palmer, T. & Lithgow, T., May 2021, In: mBio. 12, 3, 15 p., e0130221.Research output: Contribution to journal › Article › Research › peer-review
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Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation
Liu, Y., Zhu, Y. H., Song, X., Song, J. & Yu, D. J., Sept 2021, In: Briefings in Bioinformatics. 22, 5, p. 1-14 14 p.Research output: Contribution to journal › Article › Research › peer-review
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2020
Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM
Wright, A., Deane-Alder, K., Marschall, E., Bamert, R., Venugopal, H., Lithgow, T., Lupton, D. W. & Belousoff, M. J., 12 Jun 2020, In: ACS Pharmacology and Translational Science. 3, 3, p. 425-432 8 p.Research output: Contribution to journal › Article › Research › peer-review
Open Access31 Link opens in a new tab Citations (Scopus) -
DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites
Li, F., Chen, J., Leier, A., Marquez-Lago, T., Liu, Q., Wang, Y., Revote, J., Smith, A. I., Akutsu, T., Webb, G. I., Kurgan, L. & Song, J., 15 Feb 2020, In: Bioinformatics. 36, 4, p. 1057-1065 9 p.Research output: Contribution to journal › Article › Research › peer-review
113 Link opens in a new tab Citations (Scopus) -
Dynamic epidemiology and virulence characteristics of carbapenem-resistant klebsiella pneumoniae in wenzhou, China from 2003 to 2016
Zhao, Y., Zhang, S., Fang, R., Wu, Q., Li, J., Zhang, Y., Rocker, A., Cao, J., Lithgow, T. & Zhou, T., 31 Mar 2020, In: Infection and Drug Resistance. 13, p. 931-940 10 p.Research output: Contribution to journal › Article › Research › peer-review
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Forensic genomics of a novel klebsiella quasipneumoniae type from a neonatal intensive care unit in China reveals patterns of colonization, evolution and epidemiology
Perlaza-Jiménez, L., Wu, Q., Torres, V. V. L., Zhang, X., Li, J., Rocker, A., Lithgow, T., Zhou, T. & Vijaykrishna, D., 15 Sept 2020, In: Microbial Genomics. 6, 10, 10 p., 000433.Research output: Contribution to journal › Article › Research › peer-review
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Formation and function of bacterial organelles
Greening, C. & Lithgow, T., Dec 2020, In: Nature Reviews Microbiology. 18, 12, p. 677-689 13 p.Research output: Contribution to journal › Review Article › Research › peer-review
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Global trends in proteome remodeling of the outer membrane modulate antimicrobial permeability in Klebsiella pneumoniae
Rocker, A., Lacey, J. A., Belousoff, M. J., Wilksch, J. J., Strugnell, R. A., Davies, M. R. & Lithgow, T., 14 Apr 2020, In: mBio. 11, 2, 16 p., e00603-20.Research output: Contribution to journal › Article › Research › peer-review
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Investigation of LuxS-mediated quorum sensing in Klebsiella pneumoniae
Chen, L., Wilksch, J. J., Liu, H., Zhang, X., Torres, V. V. L., Bi, W., Mandela, E., Cao, J., Li, J., Lithgow, T. & Zhou, T., 28 Jan 2020, In: Journal of Medical Microbiology. 69, 3, p. 402-413 12 p.Research output: Contribution to journal › Article › Research › peer-review
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Mapping bacterial effector arsenals: in vivo and in silico approaches to defining the protein features dictating effector secretion by bacteria
Lee, Y. W., Wang, J., Newton, H. J. & Lithgow, T., Oct 2020, In: Current Opinion in Microbiology. 57, p. 13-21 9 p.Research output: Contribution to journal › Review Article › Research › peer-review
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PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins
Wang, J., Dai, W., Li, J., Xie, R., Dunstan, R. A., Stubenrauch, C., Zhang, Y. & Lithgow, T., 27 May 2020, In: Nucleic Acids Research. 48, W1, p. W348-W357 10 p.Research output: Contribution to journal › Article › Research › peer-review
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PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins
Zhang, Y., Yu, S., Xie, R., Li, J., Leier, A., Marquez-Lago, T. T., Akutsu, T., Smith, A. I., Ge, Z., Wang, J., Lithgow, T. & Song, J., 1 Feb 2020, In: Bioinformatics. 36, 3, p. 704-712 9 p.Research output: Contribution to journal › Article › Research › peer-review
49 Link opens in a new tab Citations (Scopus) -
The architecture and stabilisation of flagellotropic tailed bacteriophages
Hardy, J. M., Dunstan, R. A., Grinter, R., Belousoff, M. J., Wang, J., Pickard, D., Venugopal, H., Dougan, G., Lithgow, T. & Coulibaly, F., 27 Jul 2020, In: Nature Communications. 11, 1, 11 p., 3748.Research output: Contribution to journal › Article › Research › peer-review
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The crystal structure of the TonB-dependent transporter YncD reveals a positively charged substrate-binding site
Grinter, R. & Lithgow, T., 1 May 2020, In: Acta Crystallographica Section D: Structural Biology. 76, p. 484-495 12 p.Research output: Contribution to journal › Article › Research › peer-review
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2019
An Outbreak of Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae in an Intensive Care Unit of a Major Teaching Hospital in Wenzhou, China
Zhao, Y., Zhang, X., Torres, V. V. L., Liu, H., Rocker, A., Zhang, Y., Wang, J., Chen, L., Bi, W., Lin, J., Strugnell, R. A., Zhang, S., Lithgow, T., Zhou, T. & Cao, J., 19 Aug 2019, In: Frontiers in Public Health. 7, 11 p., 229.Research output: Contribution to journal › Article › Research › peer-review
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Bastion3: A two-layer ensemble predictor of type III secreted effectors
Wang, J., Li, J., Yang, B., Xie, R., Marquez-Lago, T. T., Leier, A., Hayashida, M., Akutsu, T., Zhang, Y., Chou, K.-C., Selkrig, J., Zhou, T., Song, J. & Lithgow, T., 1 Jun 2019, In: Bioinformatics. 35, 12, p. 2017-2028 12 p., bty914.Research output: Contribution to journal › Article › Research › peer-review
70 Link opens in a new tab Citations (Scopus) -
cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria
Belousoff, M. J., Venugopal, H., Wright, A., Seoner, S., Stuart, I., Stubenrauch, C., Bamert, R. S., Lupton, D. W. & Lithgow, T., 5 Mar 2019, In: ChemMedChem. 14, 5, p. 527-231 5 p.Research output: Contribution to journal › Article › Research › peer-review
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Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches
Wang, J., Yang, B., An, Y., Marquez-Lago, T., Leier, A., Wilksch, J., Hong, Q., Zhang, Y., Hayashida, M., Akutsu, T., Webb, G. I., Strugnell, R. A., Song, J. & Lithgow, T., 21 May 2019, In: Briefings in Bioinformatics. 20, 3, p. 931-951 21 p.Research output: Contribution to journal › Article › Research › peer-review
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The multifunctional enzyme S-adenosylhomocysteine/methylthioadenosine nucleosidase is a key metabolic enzyme in the virulence of Salmonella enterica var Typhimurium
Husna, A. U., Wang, N., Wilksch, J. J., Newton, H. J., Hocking, D. M., Hay, I. D., Cobbold, S. A., Davies, M. R., McConville, M. J., Lithgow, T. & Strugnell, R. A., 29 Nov 2019, In: Biochemical Journal. 476, 22, p. 3435-3453 19 p.Research output: Contribution to journal › Article › Research › peer-review
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The TAM: A Translocation and Assembly Module of the β-Barrel Assembly Machinery in Bacterial Outer Membranes
Stubenrauch, C. J. & Lithgow, T., 27 Feb 2019, In: EcoSal Plus. 8, 2, p. 1-7 7 p.Research output: Contribution to journal › Article › Research › peer-review
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The TAM: A translocation and assembly module of the β-barrel assembly machinery in bacterial outer membranes
Stubenrauch, C. J. & Lithgow, T., 1 Jan 2019, Protein Secretion in Bacteria. Sandkvist, M., Cascales, E. & Christie, P. J. (eds.). Washington, DC, USA: Wiley-Academy, p. 103-111 9 p.Research output: Chapter in Book/Report/Conference proceeding › Chapter (Book) › Other › peer-review
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Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods
Li, F., Wang, Y., Li, C., Marquez-Lago, T. T., Leier, A., Rawlings, N. D., Haffari, G., Revote, J., Akutsu, T., Chou, K.-C., Purcell, A. W., Pike, R. N., Webb, G. I., Smith, A. I., Lithgow, T., Daly, R. J., Whisstock, J. C. & Song, J., 27 Nov 2019, In: Briefings in Bioinformatics. 20, 6, p. 2150-2166 17 p.Research output: Contribution to journal › Article › Research › peer-review
77 Link opens in a new tab Citations (Scopus) -
2018
An investigation into the Omp85 protein BamK in hypervirulent Klebsiella pneumoniae, and its role in outer membrane biogenesis
Torres, V. V. L., Heinz, E., Stubenrauch, C. J., Wilksch, J. J., Cao, H., Yang, J., Clements, A., Dunstan, R. A., Alcock, F., Webb, C. T., Dougan, G., Strugnell, R. A., Hay, I. D. & Lithgow, T., Sept 2018, In: Molecular Microbiology. 109, 5, p. 584-599 16 p.Research output: Contribution to journal › Article › Research › peer-review
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Bastion6: A bioinformatics approach for accurate prediction of type VI secreted effectors
Wang, J., Yang, B., Leier, A., Marquez-Lago, T., Hayashida, M., Rocker, A., Zhang, Y., Akutsu, T., Chou, K.-C., Strugnell, R. A., Song, J. & Lithgow, T., 1 Jan 2018, In: Bioinformatics. 34, 15, p. 2546-2555 10 p.Research output: Contribution to journal › Article › Research › peer-review
Open AccessFile108 Link opens in a new tab Citations (Scopus) -
Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI
An, Y., Wang, J., Li, C., Leier, A., Marquez-Lago, T., Wilksch, J., Zhang, Y., Webb, G. I., Song, J. & Lithgow, T., 1 Jan 2018, In: Briefings in Bioinformatics. 19, 1, p. 148-161 14 p., bbw100.Research output: Contribution to journal › Article › Research › peer-review
57 Link opens in a new tab Citations (Scopus) -
FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants
Grinter, R., Hay, I. D., Song, J., Wang, J., Teng, D., Dhanesakaran, V., Wilksch, J. J., Davies, M. R., Littler, D., Beckham, S. A., Henderson, I. R., Strugnell, R. A., Dougan, G. & Lithgow, T., 2 Aug 2018, In: PLoS Biology. 16, 8, 21 p., e2006026.Research output: Contribution to journal › Article › Research › peer-review
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Structure and membrane topography of the vibrio-type secretin complex from the type 2 secretion system of enteropathogenic Escherichia coli
Hay, I. D., Belousoff, M. J., Dunstan, R. A., Bamert, R. S. & Lithgow, T., 1 Mar 2018, In: Journal of Bacteriology. 200, 5, 15 p., e00521-17.Research output: Contribution to journal › Article › Research › peer-review
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The WD40 Protein BamB Mediates Coupling of BAM Complexes into Assembly Precincts in the Bacterial Outer Membrane
Gunasinghe, S. D., Shiota, T., Stubenrauch, C. J., Schulze, K. E., Webb, C. T., Fulcher, A. J., Dunstan, R. A., Hay, I. D., Naderer, T., Whelan, D. R., Bell, T. D. M., Elgass, K. D., Strugnell, R. A. & Lithgow, T., 29 May 2018, In: Cell Reports. 23, 9, p. 2782-2794 13 p.Research output: Contribution to journal › Article › Research › peer-review
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2017
Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function
Stubenrauch, C. J., Dougan, G., Lithgow, T. & Heinz, E., 15 Nov 2017, In: Open Biology. 7, 11, 10 p., 170144.Research output: Contribution to journal › Article › Research › peer-review
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Extensively drug-resistant klebsiella pneumoniae causing nosocomial bloodstream infections in China: Molecular investigation of antibiotic resistance determinants, Informing therapy, and clinical outcomes
Bi, W., Liu, H., Dunstan, R. A., Li, B., Torres, V. V. L., Cao, J., Chen, L., Wilksch, J. J., Strugnell, R. A., Lithgow, T. & Zhou, T., 30 Jun 2017, In: Frontiers in Microbiology. 8, 12 p., 1230.Research output: Contribution to journal › Article › Research › peer-review
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Knowledge-Transfer learning for prediction of matrix metalloprotease substrate-cleavage sites
Wang, Y., Song, J., Marquez-Lago, T., Leier, A., Li, C., Lithgow, T., Webb, G. I. & Shen, H.-B., 1 Dec 2017, In: Scientific Reports. 7, 1, 5755.Research output: Contribution to journal › Article › Research › peer-review
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Phylogenetic analysis of Klebsiella pneumoniae from hospitalized children, Pakistan
Ejaz, H., Wang, N., Wilksch, J. J., Page, A. J., Cao, H., Gujaran, S., Keane, J. A., Lithgow, T., Ul-Haq, I., Dougan, G., Strugnell, R. A. & Heinz, E., 1 Nov 2017, In: Emerging Infectious Diseases. 23, 11, p. 1872-1875 4 p.Research output: Contribution to journal › Article › Research › peer-review
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POSSUM: A bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles
Wang, J., Yang, B., Revote, J., Leier, A., Marquez-Lago, T. T., Webb, G., Song, J., Chou, K.-C. & Lithgow, T., 1 Jan 2017, In: Bioinformatics. 33, 17, p. 2756-2758 3 p.Research output: Contribution to journal › Article › Research › peer-review
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Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori
Webb, C. T., Chandrapala, D., Oslan, S. N., Bamert, R. S., Grinter, R. D., Dunstan, R. A., Gorrell, R. J., Song, J., Strugnell, R. A., Lithgow, T. & Kwok, T., 1 Dec 2017, In: MicrobiologyOpen. 6, 6, 17 p., e00513.Research output: Contribution to journal › Article › Research › peer-review
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SecretEPDB: A comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems
An, Y., Wang, J., Li, C., Revote, J., Zhang, Y., Naderer, T., Hayashida, M., Akutsu, T., Webb, G. I., Lithgow, T. & Song, J., 23 Jan 2017, In: Scientific Reports. 7, 10 p., 41031.Research output: Contribution to journal › Article › Research › peer-review
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Structural basis for linezolid binding site rearrangement in the Staphylococcus aureus ribosome
Belousoff, M. J., Eyal, Z., Radjainia, M., Ahmed, T., Bamert, R. S., Matzov, D., Bashan, A., Zimmerman, E., Mishra, S., Cameron, D., Elmlund, H., Peleg, A. Y., Bhushan, S., Lithgow, T. & Yonath, A., 9 May 2017, In: mBio. 8, 3, 7 p., e00395-17.Research output: Contribution to journal › Article › Research › peer-review
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Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery
Bamert, R. S., Lundquist, K., Hwang, H., Webb, C. T., Shiota, T., Stubenrauch, C. J., Belousoff, M. J., Goode, R. J. A., Schittenhelm, R. B., Zimmerman, R., Jung, M., Gumbart, J. C. & Lithgow, T., 1 Oct 2017, In: Molecular Microbiology. 106, 1, p. 142-156 15 p.Research output: Contribution to journal › Article › Research › peer-review
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Structural basis of type 2 secretion system engagement between the inner and outer bacterial membranes
Hay, I. D., Belousoff, M. J. & Lithgow, T., 17 Oct 2017, In: mBio. 8, 5, 6 p., e01344-17.Research output: Contribution to journal › Article › Research › peer-review
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